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ABSTRACT: Although the quantitative trait locus (QTL) on chromosome 18 (BTA18) associated with paternal calving ease and stillbirth in Holstein Friesian cattle and its cross has been known for over 20 years, to our knowledge, the exact causal genetic sequence has yet escaped identification. The aim of this study was to re-examine the region of the published QTL on BTA18 and to investigate the possible reasons behind this elusiveness. For this purpose, we carried out a combined linkage disequilibrium and linkage analysis using genotyping data of 2,697 German Holstein Friesian (HF) animals and subsequent whole-genome sequencing (WGS) data analyses and genome assembly of HF samples. We confirmed the known QTL in the 95% confidence interval of 1.089 Mbp between 58.34 and 59.43 Mbp on BTA18. Additionally, these 4 SNPs in the near-perfect linkage disequilibrium with the QTL haplotype were identified: rs381577268 (on 57,816,137 bp, C/T), rs381878735 (on 59,574,329 bp, A/T), rs464221818 (on 59,329,176 bp, C/T), and rs472502785 (on 59,345,689 bp, T/C). Search for the causal mutation using short and long-read sequences, and methylation data of the BTA18 QTL region did not reveal any candidates though. The assembly showed problems in the region, as well as an abundance of segmental duplications within and around the region. Taking the QTL of BTA18 in Holstein cattle as an example, the data presented in this study comprehensively characterize the genomic features that could also be relevant for other such elusive QTL in various other cattle breeds and livestock species as well.

In Europe, the Alpine ibex (Capra ibex) was on the brink of extinction in the 19th century. Therefore, different conservation measures were implemented, and several reintroductions were made in the Alpine arc, starting from the only surviving population in Gran Paradiso, Italy. An extreme historical bottleneck and additional reintroductions have strongly shaped the genetic make-up of recent populations, resulting in significant genetic drift and profound inbreeding across the species range. To support science-based conservation actions, molecular methods have been increasingly used. However, such analyses did not include populations in Slovenia. We analysed neutral loci (partial fragment of mitochondrial cytochrome b, mtDNA) and the adaptive major histocompatibility complex (MHC DRB exon 2) of the Alpine ibex from both Slovenian populations (Julian and Kamnik-Savinja Alps) to understand how past reintroductions and recent management have affected the genetic diversity of the species. Results showed that both populations are genetically severely depleted, carrying only one mtDNA haplotype and one functional allele for MHC DRB exon 2, Caib-DRB*01. This calls for further conservation actions, including the reintroduction of individuals with different genetic background. However, the Alpine ibex is currently considered a non-native species in Slovenia, which makes conservation actions extremely difficult and threatens the long-term survival of the species. Therefore, scientists and population managers are urging policy/decision makers to change the status of the species to the native one and consequently to allow reintroductions. These appeals are supported by previous archaeological data on the existence of bones assigned to Alpine ibex in the Julian Alps, and evidence of severe genetic depletion in current ibex populations confirmed in this study. PRVI VPOGLED V GENETSKO RAZNOLIKOST ALPSKEGA KOZOROGA (Capra ibex) V SLOVENIJI Izvleček: V Evropi je bil alpski kozorog (Capra ibex) v 19. stoletju na robu izumrtja. Izvajali so se različni ukrepi za njegovo ohranjanje. V alpskem loku je bilo izvedenih več ponovnih naselitev, najprej z edino ohranjeno populacijo v kraju Gran Paradiso v Italiji. Izredna okrnjenost vrste v preteklosti in dodatne ponovne naselitve so močno vplivale na genetsko sestavo populacije, kar je povzročilo znaten genetski zdrs in parjenje v sorodstvu na celotnem območju vrste. V podporo znanstveno utemeljenim ukrepom ohranjanja se vse pogosteje uporabljajo molekularne metode, vendar takšne analize niso vključevale populacij v Sloveniji. Da bi razumeli, kako je ponovno naseljevanje in nedavno upravljanje vplivalo na genetsko raznolikost vrste, smo analizirali nevtralne lokuse (delni fragment mitohondrijskega citokroma b, mtDNA) in adaptivni poglavitni histokompatibilnostni kompleks (MHC DRB ekson 2) alpskega kozoroga iz obeh slovenskih populacij (Julijske in Kamniško-Savinjske Alpe). Rezultati so pokazali, da sta obe populaciji genetsko zelo osiromašeni, saj nosita le en haplotip mtDNA in en funkcionalni alel za MHC DRB ekson 2, Caib-DRB*01. Zato so potrebni nadaljnji ukrepi za ohranjanje, vključno s ponovno naselitvijo živali z drugačnim genetskim ozadjem. Vendar alpski kozorog v Sloveniji trenutno velja za tujerodno vrsto, kar zelo otežuje ukrepe za njegovo ohranitev in ogroža dolgoročno preživetje vrste. Znanstveniki in upravljavci populacij zato pozivajo politike/odločevalce, naj spremenijo status vrste v avtohtono in posledično omogočijo ponovno naselitev. Ti pozivi so podprti s predhodnimi arheološkimi podatki o obstoju kosti alpskega kozoroga v Julijskih Alpah in z dokazi o izraziti genetski osiromašenosti sedanjih populacij kozoroga, potrjenimi v tej študiji. Ključne besede: Capra ibex; mitohondrijska DNA; MHC DRB exon2; ponovna naselitev; upravljanje

Using SNP-association analysis and genetic mapping, a SNP and an insertion in and close to HOXB13 associated with short tail length is identified in Merino sheep, which may be a target for safely selecting shorter tails and improving sheep welfare.

Adolescents' interests and goals for pursuing a career in the environmental, social and economic sustainability domains were explored within the Social Cognitive Career Theory (SCCT) framework. Respondents were secondary school graduates from Croatia who participated in an online study (N = 582). Using SEM, the SCCT model was confirmed as an adequate framework for conceptualizing the origins of career interests and goals in the three sustainability domains, especially with contextual supports and barriers included as both direct and indirect effects (via learning experiences, self-efficacy, and outcome expectations) on goals. Implications of results for career guidance practice and policies are discussed.

Abstract The contribution of domestic cattle in human societies is enormous, making cattle, along with other essential benefits, the economically most important domestic animal in the world today. To expand existing knowledge on cattle domestication and mitogenome diversity, we performed a comprehensive complete mitogenome analysis of the species (802 sequences, 114 breeds). A large sample was collected in South‐east Europe, an important agricultural gateway to Europe during Neolithization and a region rich in cattle biodiversity. We found 1725 polymorphic sites (810 singletons, 853 parsimony‐informative sites and 57 indels), 701 unique haplotypes, a haplotype diversity of 0.9995 and a nucleotide diversity of 0.0015. In addition to the dominant T3 and several rare haplogroups (Q, T5, T4, T2 and T1), we have identified maternal line in Austrian Murbodner cattle that possess surviving aurochs’ mitochondria haplotype P1 that diverged prior to the Neolithization process. This is convincing evidence for rare female‐mediated adaptive introgression of wild aurochs into domesticated cattle in Europe. We revalidated the existing haplogroup classification and provided Bayesian phylogenetic inference with a more precise estimated divergence time than previously available. Occasionally, classification based on partial mitogenomes was not reliable; for example, some individuals with haplogroups P and T5 were not recognized based on D‐loop information. Bayesian skyline plot estimates (median) show that the earliest population growth began before domestication in cattle with haplogroup T2, followed by Q (~10.0–9.5 kyBP), whereas cattle with T3 (~7.5 kyBP) and T1 (~3.0–2.5 kyBP) expanded later. Overall, our results support the existence of interactions between aurochs and cattle during domestication and dispersal of cattle in the past, contribute to the conservation of maternal cattle diversity and enable functional analyses of the surviving aurochs P1 mitogenome.

Abstract Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.

Argali (Ovis ammon), the largest species among all wild sheep, is native to mountainous regions of Central and East Asia, spreading mainly throughout such countries as Tajikistan, Kyrgyzstan, Kazakhstan, Afghanistan, Mongolia, Russia and China. Intraspecific taxonomy of argali remains unclear, and currently, most researchers recognize up to nine subspecies. The aim of our work was to investigate the phylogenetic relationship between populations of O. ammon based on genome-wide SNP analysis. Five subspecies, Altai (O. a. ammon) (n = 6), Gobi (O. a. darwini) (n = 5), Pamir (O. a. polii) (n = 12), Tian Shan (O.a. karelini) (n = 15) and Kyzylkum (O. a. severtzovi) (n = 4), were genotyped using Illumina OvineHD BeadChip. In addition, complete mitogenome sequences from 30 of those samples were obtained. After quality control procedures, 65,158 SNPs were selected for the subsequent analyses. Neighbor-Net dendrogram and principal component analysis (PCA) revealed that the five subspecies could be grouped into four clusters. It was shown that a population from Altai formed a cluster with Gobi subspecies. The highest pairwise FST genetic distance was between O. a. ammon and O. a. severtzovi (0.421) and the lowest were between O. a. polii and O.a. karelini (0.083) and between O. a. ammon and O. a. darwini (0.040) subspecies. Genetic diversity was higher in Central Asian argali as compared to East Asian populations. O. a. severtzovi had an admixed origin and consisted of two genetic components—73.5 ± 0.2% of O. a. polli and 26.5 ± 0.2% of urial (O. vignei). TreeMix analysis revealed a migration event from urial to O. a. severtzovi argali. The analysis of complete mitogenomes supported the results based on whole-genome genotyping. Considering that all the mtDNA sequences of O. a severtzovi belonged to O. ammon and not to O. vignei, we concluded that gene flow in this group was associated with urial males. As this is only the first work on intraspecific taxonomy and genetic diversity of argali based on genome-wide SNP genotyping and the analysis of complete mitogenomes, we suggest that more genetic studies are needed to clarify the status of Gobi and Tian Shan argali.

A comprehensive study of the indigenous Cretan sheep breeds was conducted involving both body measurements and genetic analyses. Body measurements of female sheep (Anogia (n=7); Asterousia (n=23); Sfakia (n=17) and Sitia (n=43)) included withers height, body length, ear length, tail length and girth, and body weight. Results indicated that the Sfakia breed had the highest withers height (62.7 ± 2.4 cm) while the Sitia breed had the lowest (59.1 ± 5.3 cm). In addition, the Sfakia breed showed the greatest body length (65.4 ± 5.5 cm), and the Sitia breed the smallest (60.8 ± 4.3 cm). In terms of body weight, the Sfakia breed was the heaviest (38 ± 4.2 kg) and the Anogia breed the lightest (21 ± 2.5 kg). For genetic identification, blood was sampled from 25 Anogia, 27 Asterousia, 31 Sfakia, 12 Sitia, 58 Kasos Island and 15 Karpathos Island sheep individuals. Genotypes of over 45,000 Single Nucleotide Polymorphisms (SNPs) were obtained for each breed, using the OvineSNP50 BeadChip (Illumina). Observed and expected heterozygosity, allelic richness, and the inbreeding coefficient were calculated. The highest observed heterozygosity based on SNP haplotype blocks was in the Anogia and Sitia breeds (0.78), while Anogia also had the highest expected heterozygosity (0.81) and allelic richness (7.53). The highest genomic inbreeding coefficient (0.175) was estimated in the Karpathos population and the lowest (0.062) in the Anogia breed. Genetic relatedness and distances among the breeds/populations were analyzed and depicted in phylogenetic trees, revealing significant insights into the genetic diversity and relationships of these sheep populations. [ABSTRACT FROM AUTHOR]

Abstract Background The indigenous cattle populations from Greece and Cyprus have decreased to small numbers and are currently at risk of extinction due to socio-economic reasons, geographic isolation and crossbreeding with commercial breeds. This study represents the first comprehensive genome-wide analysis of 10 indigenous cattle populations from continental Greece and the Greek islands, and one from Cyprus, and compares them with 104 international breeds using more than 46,000 single nucleotide polymorphisms (SNPs). Results We estimated several parameters of genetic diversity (e.g. heterozygosity and allelic diversity) that indicated a severe loss of genetic diversity for the island populations compared to the mainland populations, which is mainly due to the declining size of their population in recent years and subsequent inbreeding. This high inbreeding status also resulted in higher genetic differentiation within the Greek and Cyprus cattle group compared to the remaining geographical breed groups. Supervised and unsupervised cluster analyses revealed that the phylogenetic patterns in the indigenous Greek breeds were consistent with their geographical origin and historical information regarding crosses with breeds of Anatolian or Balkan origin. Cyprus cattle showed a relatively high indicine ancestry. Greek island populations are placed close to the root of the tree as defined by Gir and the outgroup Yak, whereas the mainland breeds share a common historical origin with Buša. Unsupervised clustering and D-statistics analyses provided strong support for Bos indicus introgression in almost all the investigated local cattle breeds along the route from Anatolia up to the southern foothills of the Alps, as well as in most cattle breeds along the Apennine peninsula to the southern foothills of the Alps. Conclusions All investigated Cyprus and Greek breeds present complex mosaic genomes as a result of historical and recent admixture events between neighbor and well-separated breeds. While the contribution of some mainland breeds to the genetic diversity pool seems important, some island and fragmented mainland breeds suffer from a severe decline of population size and loss of alleles due to genetic drift. Conservation programs that are a compromise between what is feasible and what is desirable should focus not only on the still highly diverse mainland breeds but also promote and explore the conservation possibilities for island breeds.

Abstract Background Breeding genetically hornless, i.e. polled, cattle provides an animal welfare-friendly and non-invasive alternative to the dehorning of calves. However, the molecular regulation of the development of horns in cattle is still poorly understood. Studying genetic characters such as polledness and scurs, can provide valuable insights into this process. Scurs are hornlike formations that occur occasionally in a wide variety of sizes and forms as an unexpected phenotype when breeding polled cattle. Methods We present a unique dataset of 885 Holstein–Friesian cattle with polled parentage. The horn phenotype was carefully examined, and the phenotypic heterogeneity of the trait is described. Using a direct gene test for polledness, the polled genotype of the animals was determined. Subsequently, the existence of a putative scurs locus was investigated using high-density genotype data of a selected subset of 232 animals and two mapping approaches: mixed linear model-based association analyses and combined linkage disequilibrium and linkage analysis. Results The results of an exploratory data analysis indicated that the expression of scurs depends on age at phenotyping, sex and polled genotype. Scurs were more prevalent in males than in females. Moreover, homozygous polled animals did not express any pronounced scurs and we found that the Friesian polled allele suppresses the development of scurs more efficiently than the Celtic polled allele. Combined linkage and linkage disequilibrium mapping revealed four genome-wide significant loci that affect the development of scurs, one on BTA5 and three on BTA12. Moreover, suggestive associations were detected on BTA16, 18 and 23. The mixed linear model-based association analysis supports the results of the combined linkage and linkage disequilibrium analysis. None of the mapping approaches provided convincing evidence for a monogenic inheritance of scurs. Conclusions Our results contradict the initial and still broadly accepted model for the inheritance of horns and scurs. We hypothesise an oligogenetic model to explain the development of scurs and polledness.

Large-animal models for Duchenne muscular dystrophy (DMD) are crucial for the evaluation of diagnostic procedures and treatment strategies. Pigs cloned from male cells lacking DMD exon 52 (DMDΔ52) exhibit molecular, clinical and pathological hallmarks of DMD, but die before sexual maturity and cannot be propagated by breeding. Therefore, we generated female DMD+/− carriers. A single founder animal had 11 litters with 29 DMDY/−, 34 DMD+/− as well as 36 male and 29 female wild-type offspring. Breeding with F1 and F2 DMD+/− carriers resulted in an additional 114 DMDY/− piglets. With intensive neonatal management, the majority survived for 3-4 months, providing statistically relevant cohorts for experimental studies. Pathological investigations and proteome studies of skeletal muscles and myocardium confirmed the resemblance to human disease mechanisms. Importantly, DMDY/− pigs displayed progressive myocardial fibrosis and increased expression of connexin-43, associated with significantly reduced left ventricular ejection fraction, at 3 months. Furthermore, behavioral tests provided evidence for impaired cognitive ability. Our breeding cohort of DMDΔ52 pigs and standardized tissue repositories provide important resources for studying DMD disease mechanisms and for testing novel treatment strategies.

The present study examines current social representations associated with the origins of the Great War, a major event that has profoundly affected Europe. A survey conducted in 20 European countries (N = 1906 students in social sciences) shows a high consensus: The outbreak of the war is attributed to the warring nations’ leaders while the responsibility of the populations is minimized. Building on the concept of social representation of history (Liu & Hilton, 2005), we suggest that the social representations of the Great War fulfill social psychological functions in contemporary Europe. We suggest that WWI may function as a charter for European integration. Their content also suggests a desire to distinguish a positively valued ingroup ("the people") from powerful elites, construed as an outgroup.

Abstract Background It has been known for almost a century that the belted phenotype in cattle follows a pattern of dominant inheritance. In 2009, the approximate position of the belt locus in Brown Swiss cattle was mapped to a 922-kb interval on bovine chromosome 3 and, subsequently, assigned to a 336-kb haplotype block based on an animal set that included, Brown Swiss, Dutch Belted (Lakenvelder) and Belted Galloway individuals. A possible candidate gene in this region i.e. HES6 was investigated but the causal mutation remains unknown. Thus, to elucidate the causal mutation of this prominent coat color phenotype, we decided to remap the belted phenotype in an independent animal set of several European bovine breeds, i.e. Gurtenvieh (belted Brown Swiss), Dutch Belted and Belted Galloway and to systematically scan the candidate region. We also checked the presence of the detected causal mutation in the genome of belted individuals from a Siberian cattle breed. Results A combined linkage disequilibrium and linkage analysis based on 110 belted and non-belted animals identified a candidate interval of 2.5 Mb. Manual inspection of the haplotypes in this region identified four candidate haplotypes that consisted of five to eight consecutive SNPs. One of these haplotypes overlapped with the initial 922-kb interval, whereas two were positioned proximal and one was positioned distal to this region. Next-generation sequencing of one heterozygous and two homozygous belted animals identified only one private belted candidate allele, i.e. a multiplication event that is located between 118,608,000 and 118,614,000 bp. Targeted locus amplification and quantitative real-time PCR confirmed an increase in copy number of this region in the genomes of both European (Belted Galloway, Dutch Belted and Gurtenvieh) and Siberian (Yakutian cattle) breeds. Finally, using nanopore sequencing, the exact breakpoints were determined at 118,608,362 and 118,614,132 bp. The closest gene to the candidate causal mutation (16 kb distal) is TWIST2. Conclusions Based on our findings and those of a previously published study that identified the same multiplication event, a quadruplication on bovine chromosome 3 between positions 118,608,362 and 118,614,132 bp is the most likely candidate causal mutation for the belted phenotype in cattle.

Abstract Background Russia has a diverse variety of native and locally developed sheep breeds with coarse, fine, and semi-fine wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data. Results We recorded similar observed heterozygosity (0.354–0.395) and allelic richness (1.890–1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their wool type (fine wool, semi-fine wool and coarse wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The coarse-wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran). Conclusions In this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations.

Population genomic analyses such as inference of population structure and identifying signatures of selection usually involve the application of a plethora of tools. The installation of tools and their dependencies, data transformation, or series of data preprocessing in a particular order sometimes makes the analyses challenging. While the usage of container-based technologies has significantly resolved the problems associated with the installation of tools and their dependencies, population genomic analyses requiring multistep pipelines or complex data transformation can greatly be facilitated by the application of workflow management systems such as Nextflow and Snakemake. Here, we present scalepopgen, a collection of fully automated workflows that can carry out widely used population genomic analyses on the biallelic single nucleotide polymorphism data stored in either variant calling format files or the plink-generated binary files. scalepopgen is developed in Nextflow and can be run locally or on high-performance computing systems using either Conda, Singularity, or Docker. The automated workflow includes procedures such as (i) filtering of individuals and genotypes; (ii) principal component analysis, admixture with identifying optimal K -values; (iii) running TreeMix analysis with or without bootstrapping and migration edges, followed by identification of an optimal number of migration edges; (iv) implementing single-population and pair-wise population comparison-based procedures to identify genomic signatures of selection. The pipeline uses various open-source tools; additionally, several Python and R scripts are also provided to collect and visualize the results. The tool is freely available at https://github.com/Popgen48/scalepopgen. [ABSTRACT FROM AUTHOR]

One of the prerequisites for successful organ xenotransplantation is a reasonable size match between the porcine organ and the recipient's organ to be replaced. Therefore, the selection of a suitable genetic background of source pigs is important. In this study, we investigated body and organ growth, cardiac function, and genetic diversity of a colony of Auckland Island pigs established at the Center for Innovative Medical Models (CiMM), LMU Munich. Male and female Auckland Island pig kidney cells (selected to be free of porcine endogenous retrovirus C) were imported from New Zealand, and founder animals were established by somatic cell nuclear transfer (SCNT). Morphologically, Auckland Island pigs have smaller body stature compared to many domestic pig breeds, rendering their organ dimensions well‐suited for human transplantation. Furthermore, echocardiography assessments of Auckland Island pig hearts indicated normal structure and functioning across various age groups throughout the study. Single nucleotide polymorphism (SNP) analysis revealed higher runs of homozygosity (ROH) in Auckland Island pigs compared to other domestic pig breeds and demonstrated that the entire locus coding the swine leukocyte antigens (SLAs) was homozygous. Based on these findings, Auckland Island pigs represent a promising genetic background for organ xenotransplantation. [ABSTRACT FROM AUTHOR]

Ear length in sheep (Ovis aries) shows a wide range of natural variation, from the absence of an outer ear structure (anotia), to small outer ears (microtia), to regular ear length. Up until now, the underlying genetics of this phenotype has been studied in four sheep breeds from China, Jordan and Italy. These studies revealed a broad range of genes significantly associated with ear length, potentially indicating genetic heterogeneity across breeds or geographic regions. In the current study, we performed genome‐wide SNP genotyping and haplotype‐based mapping, in a population of 340 individuals, to identify loci influencing ear length variation in additional sheep breeds from Slovenia, Croatia, Cyprus and Greece. Additionally, two previously described candidate variants were also genotyped in our mapping population. The mapping model without candidate variant genotypes revealed only one genome‐wide significant signal, which was located next to HMX1 on OAR6. This region was previously described as being associated with ear length variation in the Altay and Awassi sheep breeds. The mapping model including the candidate duplication genotype near HMX1 as a fixed effect explained the phenotypic variance on OAR6 and revealed an additional genome‐wide significant locus on OAR13 associated with ear length. Our results, combined with published evidence, suggest that a duplication in the evolutionarily conserved region near HMX1 is the major regulator of ear length in sheep breeds descended from a larger region from Central Asia, to the Middle East, Cyprus, Greece and to the Alps. This distribution suggests an ancient origin of the derived allele. [ABSTRACT FROM AUTHOR]

Abstract Background Cases of albinism have been reported in several species including cattle. So far, research has identified many genes that are involved in this eye-catching phenotype. Thus, when two paternal Braunvieh half-sibs with oculocutaneous albinism were detected on a private farm, we were interested in knowing whether their phenotype was caused by an already known gene/mutation. Results Analysis of genotyping data (50K) of the two albino individuals, their mothers and five other relatives identified a 47.61-Mb candidate haplotype on Bos taurus chromosome BTA20. Subsequent comparisons of the sequence of this haplotype with sequence data from four Braunvieh sires and the Aurochs genome identified two possible candidate causal mutations at positions 39,829,806 bp (G/A; R45Q) and 39,864,148 bp (C/T; T444I) that were absent in 1682 animals from various bovine breeds included in the 1000 bull genomes project. Both polymorphisms represent coding variants in the SLC45A2 gene, for which the human equivalent harbors numerous variants associated with oculocutaneous albinism type 4. We demonstrate an association of R45Q and T444I with the albino phenotype by targeted genotyping. Conclusions Although the candidate gene SLC45A2 is known to be involved in albinism in different species, to date in cattle only mutations in the TYR and MITF genes were reported to be associated with albinism or albinism-like phenotypes. Thus, our study extends the list of genes that are associated with bovine albinism. However, further research and more samples from related animals are needed to elucidate if only one of these two single nucleotide polymorphisms or the combination of both is the actual causal variant.

Karachaev goat (Capra hircus) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A.

Sheep are a main livestock species of Kyrgyzstan, a Central Asian country with predominating mountain terrain. The current gene pool of local sheep resources has been forming under diverse climate conditions from the era of the trading caravans of the Great Silk Road, through the Soviet period of large-scale livestock improvements, which was followed by the deep crisis at the end of the 20th century, up to now. However, not much is known about the genetic background and variability of the local sheep populations. Therefore, our aims were to provide a characterization of the population structure and genetic relations within the Kyrgyz sheep breeds and to study their genetic connections with the global sheep breeds using SNP analysis. Samples of the Alai (n = 31), Gissar (n = 30), Kyrgyz coarse wool (n = 13), Aykol (n = 31), and Tien-Shan (n = 24) breeds were genotyped with the OvineSNP50 BeadChip or the Ovine Infinium HD BeadChip (Illumina Inc., USA). The measure of inbreeding based on runs of homozygosity showed a minimum value in the Aykol breed (FROH = 0.034), while the maximum was found in the Alai breed (FROH = 0.071). Short ROH segments (ROH ≤ 4 Mb) were predominant in all breeds. Long ROH segments (ROH > 16 Mb) were absent in the Gissar breed. The Gissar and Aykol breeds had the highest values of the effective population sizes estimated for five generations ago (Ne5 = 660 and 563), whereas the Alai and Kyrgyz coarse wool displayed lower values (Ne5 = 176 and 128, respectively). The synthetic origin of the Aykol breed was clearly evidenced by all analyses applied. Based on the network and admixture analyses of the Kyrgyz and global sheep breeds, the Tien-Shan and the Russian semi-fine wool breeds demonstrated a common ancestry that most likely is due to a contribution of the Lincoln breed. The Gissar, Aykol, and Kyrgyz coarse wool breeds showed a genetic background predominating in sheep populations from Iran and China whereas the Alai demonstrated the different ancestry type. The revealed admixture patterns probably resulted from the exchange and trade during the era of the Great Silk Road, which partly overlapped with historical and archeological findings.

Currently, the intraspecific taxonomy of snow sheep (Ovis nivicola) is controversial and needs to be specified using DNA molecular genetic markers. In our previous work using whole-genome single nucleotide polymorphism (SNP) analysis, we found that the population inhabiting Kharaulakh Ridge was genetically different from the other populations of Yakut subspecies to which it was usually referred. Here, our study was aimed at the clarification of taxonomic status of Kharaulakh snow sheep using mitochondrial cytochrome b gene. A total of 87 specimens from five different geographic locations of Yakut snow sheep as well as 20 specimens of other recognized subspecies were included in this study. We identified 19 haplotypes, two of which belonged to the population from Kharaulakh Ridge. Median-joining network and Bayesian tree analyses revealed that Kharaulakh population clustered separately from all the other Yakut snow sheep. The divergence time between Kharaulakh population and Yakut snow sheep was estimated as 0.48 ± 0.19 MYA. Thus, the study of the mtDNA cytb sequences confirmed the results of genome-wide SNP analysis. Taking into account the high degree of divergence of Kharaulakh snow sheep from other groups, identified by both nuclear and mitochondrial DNA markers, we propose to classify the Kharaulakh population as a separate subspecies.

After the domestication of goats around 10,000 years before the present (BP), humans transported goats far beyond the range of their wild ancestor, the bezoar goat. This brought domestic goats into contact with many wild goat species such as ibex and markhor, enabling introgression between domestic and wild goats. To investigate this, while shedding light on the taxonomic status of wild and domestic goats, we analysed genome‐wide SNP data of 613 specimens from 14 taxonomic units, including Capra hircus, C. pyrenaica, C. ibex (from Switzerland, Austria, Germany and Slovenia), C. aegagrus aegagrus, C. a. cretica, C. h. dorcas, C. caucasica caucasica, C. c. severtzovi, C. c. cylindricornis, C. falconeri, C. sibirica sibirica, C. s. alaiana and C. nubiana, as well as Oreamnos americanus (mountain goat) as an outgroup. To trace gene flow between domestic and wild goats, we integrated genotype data of local goat breeds from the Alps as well as from countries such as Spain, Greece, Türkiye, Egypt, Sudan, Iran, Russia (Caucasus and Altai) and Pakistan. Our phylogenetic analyses displayed a clear separation between bezoar‐type and ibex‐type clades with wild goats from the Greek islands of Crete and Youra clustered within domestic goats, confirming their feral origin. Our analyses also revealed gene flow between the lineages of Caucasian tur and domestic goats that most likely occurred before or during early domestication. Within the clade of domestic goats, analyses inferred gene flow between African and Iberian goats. The detected events of introgression were consistent with previous reports and offered interesting insights into the historical relationships among domestic and wild goats. [ABSTRACT FROM AUTHOR]

Social change can be pursued by participating in a public protest, joining a community gardening initiative, or recycling at home. However, little research has investigated how individual differences in values relate to people’s engagement in different types of social change actions in the context of pro-environmental behavior. We hypothesized that values would be differentially related to different types of social change actions, based on different goals that each of these actions may have (e.g., changing one’s own behavior or influencing others). A survey among people engaged in pro-environmental activism during the 2015 United Nations Climate Change Conference supported our predictions. Specifically, we found that individual behavior and community-based actions were uniquely related to biospheric values (i.e., a key concern for nature and the environment). However, other social change actions (e.g., public protest) were uniquely related to altruistic values (i.e., a key concern for the welfare of all people), and pro-environmental lobbying was positively related to egoistic values (i.e., a key concern for power and achievement). Our findings suggest that different behaviors directed at pro-environmental social change may be based on different values. We discuss the theoretical and practical implications of these findings.

Eurasia is represented by all climatic zones and various environments. A unique breed variety of farm animals has been developed in Russia, whose territory covers a large area of the continent. A total of 69 local breeds and types of dairy, wool, and meat sheep (Ovis aries) are maintained here. However, the genetic diversity and maternal origin of these local breeds have not been comprehensively investigated. In this study, we describe the diversity and phylogeny of Russian sheep breeds inhabiting different geographical regions based on the analysis of complete sequences of mitochondrial genomes (mtDNA). Complete mtDNA sequences of the studied sheep were obtained using next-generation sequencing technology (NGS). All investigated geographical groups of sheep were characterized by high haplotype (Hd = 0.9992) and nucleotide diversity (π = 0.00378). Analysis of the AMOVA results showed that genetic diversity was majorly determined by within-population differences (77.87%). We identified 128 haplotypes in all studied sheep. Haplotypes belonged to the following haplogroups: B (64.8%), A (28.9%), C (5.5%), and D (0.8%). Haplogroup B was predominant in the western part of Russia. A high level of mtDNA polymorphism in the studied groups of local sheep indicates the presence of a significant reserve of unique genotypes in Russia, which is to be explored. [ABSTRACT FROM AUTHOR]

In this study, we present the first complete mitochondrial genomes of two species of the genus Ovis – snow sheep (Ovis nivicola) and thinhorn sheep (Ovis dalli). The mitochondrial genomes have a total length of 16,471 and 16,464 bp, respectively, including 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a non-coding region. Phylogenetic analyses using nucleotide sequences of the 13 PCGs indicated that O. nivicola and O. dalli clustered with another representative of the Pachyceros subgenus – O. canadensis, which was consistent with the previous morphological classification.

We used genome‐wide SNP data from 18 local cattle breeds from six countries of the Alpine region to characterize population structure and identify genomic regions underlying positive selection. The geographically close breeds Evolèner, Eringer, Valdostana Pezzata Nera, and Valdostana Castana were found to differ from all other Alpine breeds. In addition, three breeds, Simmental, and Original Braunvieh from Switzerland and Pinzgauer from Austria built three separate clusters. Of the 18 breeds studied, the intra‐alpine Swiss breed Evolèner had the highest average inbreeding based on runs of homozygosity (FROH) and the highest average genomic relationship within the breed. In contrast, Slovenian Cika cattle had the lowest average genomic inbreeding and the lowest average genomic relationship within the breed. We found selection signatures on chromosome 6 near known genes such as KIT and LCORL explaining variation in coat color and body size in cattle. The most prominent selection signatures were similar regardless of marker density and the breeds in the data set. In addition, using available high‐density SNP data from 14 of the breeds we identified 47 genome regions as ROH islands. The proportion of homozygous animals was higher in all studied animals of local breeds than in Holstein and Brown Swiss cattle, the two most important commercial breeds in the Alpine region. We report ROH islands near genes related to thermoregulation, coat color, production, and stature. The results of this study serve as a basis for the search for causal variants underlying adaptation to the alpine environment and other specific characteristics selected during the evolution of local Alpine cattle breeds. [ABSTRACT FROM AUTHOR]

Economic losses due to copper intoxication or deficiency is a problem encountered by sheep farmers. The aim of this study was to investigate the ovine genome for genomic regions and candidate genes responsible for variability in liver copper concentration. Liver samples were collected from slaughtered lambs of the Merinoland breed from two farms, and used for measurement of copper concentration and genome-wide association study (GWAS). A total of 45,511 SNPs and 130 samples were finally used for analysis, in which single-locus and several multi-locus GWAS (SL-GWAS; ML-GWAS) methods were employed. Gene enrichment analysis was performed for identified candidate genes to detect gene ontology (GO) terms significantly associated with hepatic copper levels. The SL-GWAS and a minimum of two ML-GWAS identified two and thirteen significant SNPs, respectively. Within genomic regions surrounding identified SNPs, we observed nine promising candidate genes such as DYNC1I2, VPS35, SLC38A9 and CHMP1A. GO terms such as lysosomal membrane, mitochondrial inner membrane and sodium:proton antiporter activity were significantly enriched. Genes involved in these identified GO terms mediate multivesicular body (MVB) fusion with lysosome for degradation and control mitochondrial membrane permeability. This reveals the polygenic status of this trait and candidate genes for further studies on breeding for copper tolerance in sheep. [ABSTRACT FROM AUTHOR]

Argali (Ovis ammon), the largest species among all wild sheep, is native to mountainous regions of Central and East Asia, spreading mainly throughout such countries as Tajikistan, Kyrgyzstan, Kazakhstan, Afghanistan, Mongolia, Russia and China. Intraspecific taxonomy of argali remains unclear, and currently, most researchers recognize up to nine subspecies. The aim of our work was to investigate the phylogenetic relationship between populations of O. ammon based on genome-wide SNP analysis. Five subspecies, Altai (O. a. ammon) (n = 6), Gobi (O. a. darwini) (n = 5), Pamir (O. a. polii) (n = 12), Tian Shan (O.a. karelini) (n = 15) and Kyzylkum (O. a. severtzovi) (n = 4), were genotyped using Illumina OvineHD BeadChip. In addition, complete mitogenome sequences from 30 of those samples were obtained. After quality control procedures, 65,158 SNPs were selected for the subsequent analyses. Neighbor-Net dendrogram and principal component analysis (PCA) revealed that the five subspecies could be grouped into four clusters. It was shown that a population from Altai formed a cluster with Gobi subspecies. The highest pairwise FST genetic distance was between O. a. ammon and O. a. severtzovi (0.421) and the lowest were between O. a. polii and O.a. karelini (0.083) and between O. a. ammon and O. a. darwini (0.040) subspecies. Genetic diversity was higher in Central Asian argali as compared to East Asian populations. O. a. severtzovi had an admixed origin and consisted of two genetic components—73.5 ± 0.2% of O. a. polli and 26.5 ± 0.2% of urial (O. vignei). TreeMix analysis revealed a migration event from urial to O. a. severtzovi argali. The analysis of complete mitogenomes supported the results based on whole-genome genotyping. Considering that all the mtDNA sequences of O. a severtzovi belonged to O. ammon and not to O. vignei, we concluded that gene flow in this group was associated with urial males. As this is only the first work on intraspecific taxonomy and genetic diversity of argali based on genome-wide SNP genotyping and the analysis of complete mitogenomes, we suggest that more genetic studies are needed to clarify the status of Gobi and Tian Shan argali. [ABSTRACT FROM AUTHOR]

Abstract Methods based on genetic distance matrices usually lose information during the process of tree-building by converting a multi-dimensional matrix into a phylogenetic tree. We applied a heuristic method of two-dimensional presentation to achieve a better resolution of the relationship between breeds and individuals investigated. Four hundred and nine individuals from nine German dog breed populations and one free-living wolf population were analysed with a marker set of 23 microsatellites. The result of the two-dimensional presentation was partly comparable with and complemented a model-based analysis that uses genotype patterns. The assignment test and the neighbour-joining tree based on allele sharing estimate allocated 99% and 97% of the individuals according to their breed, respectively. The application of the two-dimensional presentation to distances on the basis of the proportion of shared alleles resulted in comparable and further complementary insight into inferred population structure by multilocus genotype data. We expect that the inference of population structure in domesticated species with complex breeding histories can be strongly supported by the two-dimensional presentation based on the described heuristic method.

The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP) Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which potentially have had direct or indirect historical contribution to the genetic makeup of the breed of interest.

Numerous studies have found a large number of QTL associated with productive and functional traits in the cattle genome. Several Countries have already established research programs aiming at identification and exploitation of QTLs in dairy cattle (Bovenhuis and Schrooten 2002). However, the published results are not directly exploitable for MAS, as commercial interests limit the information in the literature, and because marker-QTL phase is specific to each family.

Docking the tails of lambs in long-tailed sheep breeds is a common practice worldwide. But this practice is associated with pain. Breeding for a shorter tail could offer an alternative. Therefore, this study aimed to analyze the natural tail length variation in the Merinolandschaf and to identify causal alleles for the short tail phenotype segregating within long-tailed breeds. We used SNP-based association analysis and haplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs. Genome-wide significant regions were capture sequenced in 48 lambs and comparatively analyzed in various long and short-tailed sheep breeds and wild sheep subspecies. Here we show a SNP located in the first exon of HOXB13 and a SINE element located in the promotor of HOXB13 as promising candidates. These results enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development. Using SNP-association analysis and genetic mapping, a SNP and an insertion in and close to HOXB13 associated with short tail length is identified in Merino sheep, which may be a target for safely selecting shorter tails and improving sheep welfare. [ABSTRACT FROM AUTHOR]

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae.

The insulin-like growth factor 2 receptor (IGF2R) is essential for prenatal growth regulation and shows gene dosage effects on fetal weight that can be affected by in-vitro embryo culture. Imprinted maternal expression of murine Igf2r is well documented for all fetal tissues excluding brain, but polymorphic imprinting and biallelic expression were reported for IGF2R in human. These differences have been attributed to evolutionary changes correlated with specific reproductive strategies. However, data from species suitable for testing this hypothesis are lacking. The domestic cow (Bos taurus) carries a single conceptus with a similar gestation length as human. We identified 12 heterozygous concepti informative for imprinting studies among 68 Bos taurus fetuses at Day 80 of gestation (28% term) and found predominantly maternal IGF2R expression in all fetal tissues but brain, which escapes imprinting. Inter-individual variation in allelic expression bias, i.e. expression of the repressed paternal allele relative to the maternal allele, ranged from 4.6-8.9% in heart, 4.3-10.2% in kidney, 6.1-11.2% in liver, 4.6-15.8% in lung and 3.2-12.2% in skeletal muscle. Allelic bias for mesodermal tissues (heart, skeletal muscle) differed significantly (P